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  • Contains 1 Component(s) Includes a Live Web Event on 11/28/2023 at 12:00 PM (EST)

    Real-case-scenario road maps on how to design an experiment that leverages the use of multiple core facilities will be presented. Road maps will encompass the questions a researcher should ask, considerations for experimental design, price models, and how to establish a working relationship that will establish trust, collaboration, and accountability.

    This webinar will present SRR Cores, delineate what you should expect from your local Core and what they will expect from you, and help you create a check list and workflow to help step through your next grant application seamlessly.  This webinar is geared to helping your grant proposal funding application stand out through effective use of SRR core laboratories.  Cores create a collaborative hub for projects, providing wide-ranging expertise in experimental design, methodology and budgeting; access and training on advanced technology that is cost effective, unbiased and transparent; employ best practices and data standards, reducing variables to generate objective, unbiased data; and guidance through the NIH data management and sharing policy.

     

    Real-case-scenario road maps on how to design an experiment that leverages the use of multiple core facilities will be presented.  Road maps will encompass the questions a researcher should ask, considerations for experimental design, price models, and how to establish a working relationship that will establish trust, collaboration, and accountability.

     

    Overview of Presentation:

    • Increase understanding and awareness of the support options in shared research resource core laboratories (SRR) 
    • Gain tools for facilitating conversations with SRR staff 
    • Learn how to develop a budget inclusive of SRR

    Roxann Ashworth, MHS

    Administrative Manager, Genetic Resources Core Facilities DNA Services

    Genetic Resources Core Facilities DNA Services

    Nicole White, PhD

    Director Research Operations

    Cincinnati Children's Hospital

    Sridar Chittur, BPharm, PhD, MBA

    Sheenah Mische, PhD

    Nicholas Ambulos, Jr., PhD

    Professor of Microbiology & Immunology and Medicine

    University of Maryland

    • Register
      • Regular Member - Free!
      • Early Career Member - Free!
      • Resident/Clinical Fellow Member - Free!
      • Postdoctoral Fellow Member - Free!
      • Graduate Student Member - Free!
      • Undergraduate Student Member - Free!
      • Emeritus Member - Free!
      • Life Member - Free!
      • Trainee Member - Free!
      • Nonmember - Free!
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  • Contains 1 Component(s)

    Dr. Julie R. Coleman, Dr. Shamika Ketkar, and Dr. Jinyoung Byun of the All of Us Evenings with Genetics (AoUEwG) Research Program at Baylor College of Medicine will provide training on the platform and tools to access and analyze the NIH’s All of Us data.

    The NIH’s All of Us data is one of the largest health data resources available and includes demographic, survey, electronic health record (EHR), Fitbit, genomic, and other data from over 400,000 participants with a target to grow to 1,000,000 participants. The data is extensive, currently including EHR data from over 378,000 participants, survey data from over 409,000 participants, short-read whole genomic sequencing (WGS) data from 245,400 participants, long-read WGS data from 1,040 participants, short-read WGS structural variant data from 11,400 participants, and genotyping arrays from 312,940 participants.

    The All of Us data is also one of the most diverse health data resources available, with over 50% of participants from racial and ethnic minorities and 80% of participants underrepresented in biomedical research. The All of Us Evenings with Genetics (AoUEwG) Research Program of the Department of Molecular and Human Genetics at Baylor College of Medicine is training the next generation of biomedical researchers on the platform and tools available to be used for projects leveraging data from All of Us.

    The training provided at this workshop includes the topics below:

    • An introduction to the All of Us Researcher Workbench as the online platform for accessing and analyzing the All of Us data
    • A demonstration of starting a project on the Researcher Workbench by creating a workspace and retrieving the desired datasets
    • A review of best practices for cleaning and analyzing retrieved datasets in All of Us Jupyter Notebooks that support Python and R programming languages, limited bash commands, and genomic analysis software, including Hail and Plink
    • A discussion of analyzing the genomic data in a genome-wide association study (GWAS) using Hail that is scalable and efficient, and includes principal component analyses (PCA)
    • Supplementary material to review after the workshop for continued practice and learning

    Julie R. Coleman

    Lead Bioinformatics Programmer of the All of Us Evenings with Genetics Research Program

    Department of Molecular of Human Genetics, Baylor College of Medicine

    Dr. Julie R. Coleman is the Lead Bioinformatics Programmer of the All of Us Evenings with Genetics (AoUEwG) Research Program in the Department of Molecular of Human Genetics at Baylor College of Medicine (BCM). Her PhD is in Plant Breeding and Genetics from Texas A&M University, followed by working in the seed industry for five years in breeding Brassica genetics. She then transitioned to medicine and biotechnology, briefly working in the drug discovery industry with data science and software, before joining BCM in January 20222. While at BCM, she has focused on training biomedical researchers from across the United States on the All of Us Researcher Workbench through the AoUEwG’s annual All of Us Biomedical Researcher (BR) Scholars Program. She also provides continual data science support for these researchers as they complete their projects on the Researcher Workbench.

    Shamika Ketkar

    Assistant Professor

    Department of Molecular and Human Genetics, Baylor College of Medicine

    Dr. Shamika Ketkar is an Assistant Professor in the Department of Molecular and Human Genetics at Baylor College of Medicine (BCM). She completed her doctoral training in Statistical and Human Genetics and masters training in Genetic Epidemiology from Washington University School of Medicine in St Louis Missouri (WashU). Her core research interests include understanding the genomics, transcriptomics and epigenomics of genetic disorders with an emphasis on rare undiagnosed diseases and cancers with a special focus on hematologic and bone cancers. She has a broad background in translational bioinformatics, genomics, and genetics with more than a decade of extensive experience in genomic data science at Harvard School of Public Health, WashU and BCM. She supports the All of Us Evening with Genetics Research Program as an educator and data scientist.

    Jinyoung Byun

    Assistant Professor, Institute of Clinical and Translational Research and Section of Epidemiology and Population Sciences

    Department of Medicine, Baylor College of Medicine

    Dr. Jinyoung Byun is an Assistant Professor in the Institute of Clinical and Translational Research and Section of Epidemiology and Population Sciences, Department of Medicine, at Baylor College of Medicine (BCM). She completed her postdoctoral training at the Department of Biomedical Science in the Geisel School of Medicine at Dartmouth and joined BCM in 2018. Her research focuses on understanding genetic etiology in lung cancer, liver cancer, and rare diseases in diverse populations. She joined the All of Us Evening with Genetics Research Program in 2022 and has supported the Community Engagement Partners with the All of Us Research Program introduction sessions.

    • Register
      • Regular Member - $30
      • Early Career Member - $15
      • Resident/Clinical Fellow Member - $15
      • Postdoctoral Fellow Member - $15
      • Graduate Student Member - $15
      • Undergraduate Student Member - $15
      • Emeritus Member - $15
      • Life Member - $30
      • Trainee Member - $15
      • Nonmember - $60
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  • Contains 1 Component(s)

    Stephen Mosher, Elena Ghanaim, Ava Hoffman, Anton Kovalsky and Fred Tan will discuss the new data management and sharing (DMS) policy released by the National Institutes of Health. In this workshop, attendees will learn about key data-sharing practices and take a journey through the Terra and AnVIL ecosystem to explore the features that meet NIH’s desirable characteristics.

    As biomedical data grow at an exciting pace, the ability to share them in a way that is Findable, Accessible, Interoperable, and Reusable (FAIR) has never been more important. Recognizing this need for better data practices, the National Institutes of Health (NIH) has released a new policy (NOT-OD-21-013) that requires researchers generating NIH-funded data to create a strategy and budget for data management and sharing. This plan must include the selection of a public data repository that implements desirable characteristics like unique identifiers, metadata, free and easy sharing, security, and quality assurance. Terra, an open-source bioinformatics ecosystem that includes a repository, a Data Oversight Use System (DUOS), and an analysis platform, is an ideal solution for researchers needing to comply with this new NIH policy and is already being implemented as an approved data-sharing repository by the NHGRI's Genomic Data Science Analysis, Visualization, and Informatics Lab-Space (AnVIL, NOT-HG-19-024). 

    In this interactive workshop, participants will learn about key data-sharing practices and take a journey through the Terra ecosystem to explore the features that meet NIH’s desirable characteristics. Participants will view and engage in two vignettes that discern how Terra and AnVIL can satisfy the data needs of both a large consortium and an individual research lab. In the consortium vignette, the AnVIL team will use hands-on activities to show how they are harnessing Terra features for data sharing, management, and reproducible analysis in ways that already meet NIH’s standards. In the individual lab vignette, participants can upload and share their own mock data set and metadata. Regardless of their use case, participants will walk away with the skills and confidence to include Terra/AnVIL in their data management plan. 

    By the end of the workshop, participants will learn how to: 

    1. Find and use Terra/AnVIL features that comply with NIH policy requirements

    2. Upload data to Terra/AnVIL

    3. Make data findable and accessible to promote scientific reproducibility

    Stephen Mosher

    Dr. Stephen Mosher is a Research Scientist at Johns Hopkins University. He received his Masters degree from the University of Toronto in Canada and his doctorate from the University of Tübingen in Germany. Today, Dr. Mosher serves as a program manager on the AnVIL Project (https://anvilproject.org) and the Genomic Data Science Community Network (https://www.gdscn.org).

    Elena Ghanaim

    Elena Ghanaim is the Policy Advisor for Data Science and Sharing within the Office of Genomic Data Science (OGDS) at the National Human Genome Research Institute (NHGRI). She spearheads NHGRI’s scientific data sharing policy development, oversight, and implementation. 

    Ava Hoffman

    Dr. Ava Hoffman is a Senior Staff Scientist at Fred Hutchinson Cancer Center where she is a member of the Fred Hutch Data Science Lab. She helps lead and develop outreach resources for the AnVIL Project (https://anvilproject.org) and the Genomic Data Science Community Network (https://www.gdscn.org). Her background is in genetics of non-model organisms and data science consulting for industry.

    Anton Kovalsky

    Dr. Anton Kovalsky is a Science Writer at the Broad Institute of MIT and Harvard. In this role, he authors and edits material for technical documentation, blog posts, how-to guides and workshop presentations. 

    Frederick Tan

    Frederick Tan is on the Bioinformatics Research Faculty at Carnegie Institution, Department of Embryology, and an Adjunct Assistant Professor at Johns Hopkins University, Department of Biology. He and his collaborators research mechanisms to effectively train and support diverse populations in genomic data science.

    • Register
      • Regular Member - $30
      • Early Career Member - $15
      • Resident/Clinical Fellow Member - $15
      • Postdoctoral Fellow Member - $15
      • Graduate Student Member - $15
      • Undergraduate Student Member - $15
      • Emeritus Member - $15
      • Life Member - $30
      • Trainee Member - $15
      • Nonmember - $60
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  • Contains 1 Component(s)

    Participants will gain an understanding of the new cytogenomic mapping nomenclature and see how it compare to array and sequence ISCN nomenclature.

    Participants will gain an understanding of the new cytogenomic mapping nomenclature and see how it compare to array and sequence ISCN nomenclature in different settings through worked examples and an interactive question and answer session plus an audience quiz. This workshop will fill in the current knowledge gap on how to report cytogenomic mapping results from established and emerging cytogenomic techniques. The interactive session will enable participants to see how much they have understood and where further education is required. This online workshop will be more beneficial to participants than independent learning as the workshop is interactive; enabling participants to ask questions, pose complex cases to the experts that require a solution and to work through some examples with real-time support.

    • The workshop will present examples of worked examples as well as educational tools available for laboratories and individuals.
    • The workshop will provide an interactive question and answer session of cases submitted by participants (deadline for submission 30th August). Cases will be reviewed during the September 18th workshop.
    • Finally, there will be an audience quiz and Q & A session. This online workshop will enable participants to ask questions, pose complex cases to the experts that require a solution and to work through some examples with online support.

    Learning Objectives

    • Understand the fundamental rules for cytogenomic  Genomic Mapping nomenclature
    • Practical application of the cytogenomic Genomic Mapping nomenclature in a research and diagnostic setting
    • The ability to differentiate between NGS, array and genomic mapping nomenclature 
    • To be able to formulate and use the new cytogenomic Genomic Mapping nomenclature in their own laboratories, clinical practices and in publications

    Ros Hastings, BSc, PhD, FRCPath

    Dr. Ros Hastings is the Chair of The International System for Cytogenomic Nomenclature (ISCN) and has served on the committee since 2019. She is also a consultant for the Genomics Quality Assessment Scheme a global genomics ISO accredited proficiency testing (PT) provider operated by Oxford University Hospitals NHS Foundation Trust, Oxford. GenQA offers end to end genomic testing PTs from sample receipt, analysis, interpretation and reporting through to Clinical Genetic Counselling as well as training and competency educational resources.

    Dr Hastings is a state registered clinical scientist and a Fellow of the Royal College of Pathologists. She has more than 35 years’ experience in constitutional (including prenatal), acquired and molecular cytogenomics, both in a research and diagnostic setting. Initially, Dr Hastings worked on research projects into cancer and immunological disorders at the Imperial Cancer Research Fund, London; the MRC Cytogenetics Unit, Edinburgh and the Cancer Research Campaign Laboratory, Christie Hospital, Manchester. She has also worked in four diagnostic Cytogenetics Laboratories within the UK. For past 20 years was the Director of an ISO accredited proficiency testing (PT) provider for cytogenomics and more latterly, genomics (CEQAS and GenQA).  She has previously served on the European Society for Human Genetics (ESHG) Board and the UK NEQAS Board. She was also the Chair of the ESHG Quality Committee and involved in the EU funded Eurogentest project.

    Dr Hastings has authored many publications and book chapters on genetics, NIPT, PGD, ISCN and PT. In addition, she is an author on many best practice guidelines.

     

    IS0 -International Organisation for Standardization

    Laura Conlin, PhD, FACMG

    Dr. Laura Conlin is an Associate Professor of Pathology at The Perelman School of Medicine at the University of Pennsylvania and a Director in the Genomics Diagnostic Laboratory at the at The Children’s Hospital of Philadelphia. She is board certified by the American Board of Clinical Genetics and Genomics in both Cytogenetics and Molecular Genetics.  She is a member of several professional organizations, including the American Society of Human Genetics, the American College of Medical Genetics and Genomics, and the American Cytogenomics Conference.  She has served on the ACMG/CAP Cytogenetics Resource Committee, and currently serves on the ACMG/CAP Biochemical and Molecular Genetics Committee and on the NIGMS Human Genetic Cell Repository Scientific Advisory Committee.   She is an active member of the ClinGen Recurrent CNVs Dosage Sensitivity and the Low Penetrance/Risk Allele working groups. She has been a member of the Standing Committee for the International System for Human Cytogenomic Nomenclature (ISCN) since 2019.   

    Dr. Conlin’s clinical roles involve genome-wide diagnostics in a pediatric setting, using genome-wide platforms including, SNP array platform and short read next generation sequencing, to identify and report pathogenic copy number and structural variants. Her research focuses on understanding the mechanisms of genomic alterations, with a particular interest in mosaicism and structural variation, and how to improve detection of clinically relevant structural variation using various technologies, including long-read genome sequencing and other third-generation sequencing methodologies, with the goal of implementation of these technologies into clinical diagnostic testing.

    Jean McGowan-Jordan, PhD, FCCMG

    Dr. Jean McGowan-Jordan is the Head and Laboratory Director of the CHEO Genetics Diagnostic Lab, which is an integrated regional lab with both Cytogenomic and Molecular Genetics sections. She is a Professor in the Department of Pathology and Laboratory Medicine at the University of Ottawa.  After completing fellowships in Molecular Genetics and Cytogenetics in Ottawa and Kingston Ontario, she was credentialed in both specialties through the Canadian College of Medical Geneticists (CCMG) in 2002, and has gone on to be the primary supervisor for numerous CCMG Cytogenetics Fellows. Recently, her lab introduced a stand-alone clinical test for Facioscapulohumeral Muscular Dystrophy using Optical Genome Mapping. 

    Regionally, Dr. McGowan-Jordan has worked on the Genetics Scientific Committee of the Ontario Quality Management Program – Laboratory Services, and as Chair of the CHEO/University of Ottawa CCMG Fellowship Committee.  At a national level, she has served on the CCMG Board of Directors, the CCMG Genetics and Genome Diagnostics Working Group, and Cytogenetics Committee. Internationally, Dr. McGowan-Jordan was Chair of the Standing Committee for the International System for Human Cytogenomic Nomenclature (ISCN) from 2013 to 2020, serving as lead editor of ISCN 2016 and ISCN 2020. She is currently an Advisor to this group.

    Cynthia Casson Morton, PhD

    Dr. Cynthia Casson Morton is the William Lambert Richardson Professor of Obstetrics, Gynecology and Reproductive Biology and Professor of Pathology at Harvard Medical School, Kenneth J. Ryan, M.D. Distinguished Chair in Obstetrics and Gynecology, Director of Cytogenetics and Past Director of the Biomedical Research Institute at Brigham and Women’s Hospital. Dr. Morton is an Institute Member of the Broad Institute. She holds a part-time faculty position as Chair in Auditory Genetics at the University of Manchester, UK.

    Dr. Morton is certified by the ABMGG in Ph.D. Medical Genetics, Clinical Cytogenetics and Clinical Molecular Genetics. She is a past member of the Board of Directors of the ABMGG where she served as Secretary, Treasurer and Chair of the Accreditation Committee. She was Chair of the Molecular Genetic Pathology Policy and Exam Committees of the ABMGG and the American Board of Pathology. Dr. Morton was a member of the Board of Directors of the ASHG for 12 years and served as the 2014 President. She completed a six-year tenure as Editor of The American Journal of Human Genetics and is currently Co-Editor of Human Genetics. She served as an Advisor to the Committee for the International System in Human Cytogenomics Nomenclature (ISCN) in 1994 and in 2018 was elected as a Member of the Standing Committee. Dr. Morton is a recipient of the Distinguished Cytogeneticist Award from the American Cytogenetics Conference (ACC) and is a Fellow of the AAAS.

    • Register
      • Regular Member - $30
      • Early Career Member - $15
      • Resident/Clinical Fellow Member - $15
      • Postdoctoral Fellow Member - $15
      • Graduate Student Member - $15
      • Undergraduate Student Member - $15
      • Emeritus Member - $15
      • Life Member - $30
      • Trainee Member - $15
      • Nonmember - $60
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  • Contains 2 Component(s)

    Join members of ASHG’s Membership Engagement Committee as they discuss ASHG’s Shared Interest Groups (SIGs); a place where ASHG members can collaborate with peers and discuss topics within these areas: Bioinformatics and Computational Methods, Phenotypes & Genotypes, and Emerging Laboratory Technologies.

    Join members of ASHG’s Membership Engagement Committee as they discuss ASHG’s Shared Interest Groups (SIGs); a place where ASHG members can collaborate with peers and discuss topics within these areas. The 3 SIGs ASHG currently offers are Bioinformatics and Computational Methods, Phenotypes & Genotypes, and Emerging Laboratory Technologies. After learning more about how ASHG members can get involved and benefit from the SIGs, each SIG will enter a breakout session to meet and discuss further.

    Learning Objectives

    • An overview of ASHG’s 3 SIGs; what they are and how they work. 
    • How the SIGs are beneficial to all members and why you should participate. 
    • Best practices for engaging with your peers online. 
    • A chance to dive into SIG topics through a 30-minute guided breakout session.

    Paul W. Hook, PhD

    Postdoctoral Fellow

    Johns Hopkins University

    Dr. Paul W. Hook received his Bachelor of Science degree in Biochemistry and Molecular Biology from the Pennsylvania State University in 2012. He went on to earn his PhD in Human Genetics from Johns Hopkins University School of Medicine in 2020, where his thesis work focused on pinpointing the genes and variants underlying genome-wide association signals through the use of genomic data from disease-relevant cell populations. Dr. Hook joined Winston Timp’s lab as a postdoctoral fellow in the Department of Biomedical Engineering at Johns Hopkins University in the summer of 2020. In this role, his work has focused on the development and application of new approaches for measuring different aspects of epigenetics by using long-read sequencing, including chromatin state, DNA methylation, and protein-DNA binding.

    Minna Kaikkonen-Määttä, PhD

    Professor of Cardiovascular Genomics, PI

    University of Eastern Finland

    Minna Kaikkonen-Määttä obtained her Bachelor's degree in Cellular Biology and Physiology from the Claude Bernard University Lyon 1, France, in 2002 and Master’s degree in Molecular Biology from University of Jyväskylä, Finland, in 2005. She obtained her PhD in Molecular Medicine under the supervision of Prof. Seppo Ylä-Herttuala in Kuopio in 2008. Her doctoral studies were focused on “Engineering Baculo- and Lentiviral Vectors for Enhanced and Targeted Gene Delivery”. She did her postdoctoral studies with Prof. Christopher Glass at University of California San Diego where she shifted her research focus into transcriptional gene regulation and enhancer RNAs supported by the Young Investigator Award from Leducq Foundation. She started her own lab in 2015 at the University of Eastern Finland with a focus on gene and cell level understanding of atherosclerosis using state-of-the-art next generation sequencing methods. Currently she is a Professor in Cardiovascular Genomics and runs a lab of 20 members while acting as a Vice Director of the A.I.Virtanen Research Institute and a Director of the Single Cell Genomics Core. She has published 95 peer-reviewed articles with ~5000 citations (H-index 32). She has received over 6 million in research funding and is currently supported by the European Research Council Starting Grant, Academy of Finland, Finnish Foundation for Cardiovascular Research and Sigrid Juselius Foundation. She is the President of the Finnish Society of Atherosclerosis and member of the board of European Vascular Biology Organisation, Scandinavian Society of Atherosclerosis, and Membership Engagement Committee of the American Society of Human Genetics. 

    Augusto Rojas Martinez, MD, PhD

    Senior Researcher

    The Institute for Obesity Research, Tecnologico de Monterrey (Mexico)

    Dr. Augusto Rojas-Martinez is a Senior Researcher and Professor at The Institute for Obesity Research at Tecnologico de Monterrey, Mexico. He is a physician with M.Sc. and D.Sc. degrees in Human Genetics and Molecular Biology. He did his postdoc in Gene and Cell Therapy at Baylor College of Medicine and was an honorary professor at the University of Texas Health Science Center at San Antonio, TX. Dr. Rojas-Martinez led the first efforts of preclinical and clinical gene therapy in Mexico and Latin-America. He is certified by the Mexican Council of Genetics. Dr. Rojas-Martinez is affiliated to the Mexican System of Researchers, the National Academy of Medicine of Mexico, and the Mexican Academy of Sciences. He is past-president of the Mexican Association of Human Genetics and the Latin American Network of Human Genetics.

    Douglas Dluzen, PhD (Moderator)

    Doug is Director of the Professional Development and Career Office at Johns Hopkins University. He supports trainees and post-doctoral fellows as they explore their career options and identify new career-building skillsets. He received his Ph.D. in Genetics from the Pennsylvania State University, College of Medicine and completed postdoctoral training at the National Institute on Aging, where he studied the molecular basis of health disparities. In 2017, Doug was appointed Assistant Professor of Biology at Morgan State University, where he led a research program investigating the social determinants of cardiovascular health disparities in Baltimore City. Doug has a successful record of mentoring young scientists and has a long-standing interest in the professional development of trainees, having served on training committees for the Federation of American Societies for Experimental Biology and the American Society of Human Genetics. In addition, Doug is an accomplished science writer and editor, most recently holding the position of senior science writer and editor in the Office of Communications and Public Liaison at the National Institute of Minority Health and Health Disparities, NIH.

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      • Regular Member - Free!
      • Early Career Member - Free!
      • Resident/Clinical Fellow Member - Free!
      • Postdoctoral Fellow Member - Free!
      • Graduate Student Member - Free!
      • Undergraduate Student Member - Free!
      • Emeritus Member - Free!
      • Life Member - Free!
      • Trainee Member - Free!
      • Nonmember - Free!
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  • Contains 1 Component(s)

    Dr. Shah and Ms. Genetti will discuss their paper, Actionability of unanticipated monogenic disease risks in newborn genomic screening: Findings from the BabySeq Project. The presentation will focus on the 3-5 year medical outcomes and actionability of unanticipated monogenic risks identified in newborns and their family members as part of a randomized controlled trial of newborn genomic sequencing.

    Dr. Shah and Ms. Genetti will discuss their paper, Actionability of unanticipated monogenic disease risks in newborn genomic screening: Findings from the BabySeq Project. The presentation will focus on the 3-5 year medical outcomes and actionability of unanticipated monogenic risks identified in newborns and their family members as part of a randomized controlled trial of newborn genomic sequencing.

    Overview of Presentation

    • From a randomized controlled clinical trial of comprehensive exome sequencing in 127 apparently healthy infants and 32 infants in intensive care, 17 infants (10.7%) were identified with unanticipated monogenic disease risks (uMDRs).  
    • All 17 uMDR findings were scored as moderately or highly actionable (mean 9, range: 7–11 on a 0–12 scale) and several distinctive visual patterns emerged on the radar plots.  
    • The uMDRs revealed unsuspected genetic etiologies for existing phenotypes, as well as provided risk stratification for future medical surveillance. They also prompted screening for at-risk family members, three of whom underwent cancer-risk-reducing surgeries. 
    • These findings suggest that large-scale comprehensive sequencing of newborns will reveal numerous actionable uMDRs and precipitate substantial, and in some cases lifesaving, downstream medical care in newborns and their family members. 

    Nidhi Shah, MD, FACMG

    Clinical Geneticist & Assistant Director of Center for Clinical Genomics and Advanced Technology (CGAT) in the Department of Pathology

    Dartmouth Health

    Dr. Shah is a Clinical Geneticist at Dartmouth Health Children’s, as well as the Assistant Director of Center for Clinical Genomics and Advanced Technology (CGAT) in the Department of Pathology at Dartmouth Health. She completed her Pediatrics residency at Nassau University Medical Center in Long Island, NY, followed by Clinical Genetics fellowship at Boston Children’s Hospital/ Harvard Medical School Genetics Training Program. Her research interests focus on bioinformatics pipeline development for germline analysis of exomes and genomes, as well as implementation of precision medicine in primary care through the lifetime. She is an integral part of the NIH funded Babyseq project, the first-of-its-kind randomized clinical trial designed to examine the medical, social, and economic impacts of integrating genomic sequencing into the clinical care of newborns. 

    Casie Genetti, MS, CGC

    Senior Genetic Counselor

    Boston Children's Hospital

    Casie Genetti, MS, CGC is a senior genetic counselor and project manager at Boston Children’s Hospital. She obtained her undergraduate degree from Davidson College and received her Master of Science in Genetic Counseling from Boston University Medical School in 2015.  Casie works with The Manton Center for Orphan Disease Research, The Beggs Congenital Myopathy Research Program, and The BabySeq Program at Boston Children’s Hospital focusing on rare disease diagnosis and the implementation of genomic sequencing in infancy. 

    Sara Cullinan, PhD (Moderator)

    Deputy Editor

    American Journal of Human Genetics

    • Register
      • Regular Member - Free!
      • Early Career Member - Free!
      • Resident/Clinical Fellow Member - Free!
      • Postdoctoral Fellow Member - Free!
      • Graduate Student Member - Free!
      • Undergraduate Student Member - Free!
      • Emeritus Member - Free!
      • Life Member - Free!
      • Trainee Member - Free!
    • More Information
  • Contains 1 Component(s)

    Single-cell data provides unprecedented resolution within tissues to observe the gene-expression patterns in tissues, but it also produces mountains of data stored in hundreds of tables. Participants will explore the resources and learn how to filter data along the many dimensions.

    Robert Kuhn, PhD, now retired as long-time Associate Director of the UCSC Genome Browser, will present the single-cell resources of the Genome Browser.  Single-cell data provides unprecedented resolution within tissues to observe the gene-expression patterns in tissues, but it also produces mountains of data stored in hundreds of tables.  Participants will explore the resources and learn how to filter data along the many dimensions.

     

    Learning Objectives

    •  Single-cell data offers a very specific gene expression view of the many cell types in a tissue.

    •  The UCSC Genome Browser displays single-cell data on hg38 from many projects.

    •  A new Browser feature, faceting, allows filtering of data along many dimensions.

    •  The workshop will provide guidance and experience with working with these data.


    • Register
      • Regular Member - $30
      • Early Career Member - $15
      • Resident/Clinical Fellow Member - $15
      • Postdoctoral Fellow Member - $15
      • Graduate Student Member - $15
      • Undergraduate Student Member - $15
      • Emeritus Member - $15
      • Life Member - $30
      • Trainee Member - $15
      • Nonmember - $60
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  • Contains 1 Component(s)

    David Higgins will present an overview of the Gabriella Miller Kids First Data Resource and its publicly-funded, free-to-access genomic and clinical datasets for research in pediatric cancer and structural birth defects. Attendees will follow along and be learn how to query the data, build virtual cohorts of participants, apply for access, build an analysis workflow, and analyze the data in an interactive notebook.

    The Gabriella Miller Kids First Pediatric Research Program is an NIH Common Fund initiative focused on providing large-scale clinically annotated genomic data for pediatric cancer and structural birth defect cohorts, including tumor- and germline whole genome sequencing (WGS), trio based joint-genotyping, and paired RNA sequencing of somatic tissues. The Gabriella Miller Kids First Data Resource Center (Kids First DRC; https://www.kidsfirstdrc.org) is charged with generating these datasets and empowering collaborative discovery on its data resource platforms. 26 Kids First studies are released on the Kids First Data Resource Portal, representing more than 21,000 participants and more than 1.25 PB of data, with additional datasets being released yearly. At this workshop, we present an overview of the Kids First DRC’s publicly available datasets and platforms, interactive demonstrations for how to use the Kids First Data Resource Portal (https://www.portal.kidsfirstdrc.org) to build a virtual cohort of participants and files for research, and an introduction to analyzing data on CAVATICA, Kids First’s cloud-based analysis platform (https://cavatica.sbgenomics.com).  Attendees will follow along on their own devices, using three different methods for searching  Kids First DRC’s datasets on the Kids First Data Resource Portal. The Explore Data tool allows users to search for participants of interest based on harmonized clinical phenotypes and diagnoses using the HPO and MONDO ontologies. The File Repository is designed for searching harmonized genomic files associated with these participants, from source alignments to fully processed called variants and gene expression quantification. Finally, Variant Search allows for searching for germline variants present within Kids First datasets. The Kids First Data Resource Portal is integrated with CAVATICA by Seven Bridges for running large-scale bioinformatic workflows such as alignments or variant calling. CAVATICA also supports interactive notebook-based analyses in R Studio and Jupyter Lab, all within their browser window. The session will conclude with information about how to apply for access to these publicly available datasets to help investigators of all types access and analyze genomics-scale pediatrics data as part of their research.

        • Children born with structural birth defects are more likely to be diagnosed with cancer before they turn 18, suggesting common underlying genetic causes.
        • The publicly-funded Gabriella Miller Kids First Data Resource Center produces curated clinical and genomic datasets with the goal of uncovering new insights into the biology of these conditions.
        • The Kids First Data Resource Portal is a free web tool for searching Kids First datasets and building virtual cohorts of participants based on clinical phenotypes, file metadata, or germline variants.
        • CAVATICA by Velsera is a cloud-based analysis platform that allows users to build and run large-scale bioinformatic pipelines as well as browser-based interactive analysis for further discoveries.
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      • Regular Member - $30
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      • Life Member - $30
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      • Nonmember - $60
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    2022 AJHG Awardee

    Samuel Smith, PhD sits down with Career Development Committee member, Elham Ghorbanpour, MS to discuss his 2022 AJHG Award for Outstanding Trainee Publication and more. 

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      • Early Career Member - Free!
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      • Postdoctoral Fellow Member - Free!
      • Graduate Student Member - Free!
      • Undergraduate Student Member - Free!
      • Emeritus Member - Free!
      • Life Member - Free!
      • Trainee Member - Free!
      • Nonmember - Free!
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    2022 AJHG Awardee

    Shawn Fayer, PhD sits down with Career Development Committee member, Elham Ghorbanpour, MS to discuss his 2022 AJHG Award for Outstanding Trainee Publication and more. 

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      • Regular Member - Free!
      • Early Career Member - Free!
      • Resident/Clinical Fellow Member - Free!
      • Postdoctoral Fellow Member - Free!
      • Graduate Student Member - Free!
      • Undergraduate Student Member - Free!
      • Emeritus Member - Free!
      • Life Member - Free!
      • Trainee Member - Free!
      • Nonmember - Free!
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